@article{oliva19,
title={Accounting for ambiguity in ancestral sequencereconstruction},
author={Oliva, A and Pulicani, S and Lefort, V and Br\'eh\'elin, L. and Gascuel, O. and Guindon, S},
journal={Bioinformatics},
  pages={https://www.biorxiv.org/content/early/2018/09/05/409029},
year={2019}
}

@article{etheridge2008,
  title={Drift, draft and structure: some mathematical models of evolution},
  author={Etheridge, Alison M},
  journal={Banach Center Publ.},
  volume={80},
  pages={121--144},
  year={2008}
}

@inproceedings{berestycki2009,
  title={Survival, extinction and ergodicity in a spatially continuous population model},
  author={Berestycki, N and Etheridge, A and Hutzenthaler, M},
  booktitle={Markov Proc. Rel. Fields},
  year={2009}
}
@article{barton2010,
  title={A new model for evolution in a spatial continuum},
  author={Barton, NH and Etheridge, AM and V{\'e}ber, A},
  journal={Electronic Journal of Probability},
  volume={15},
  number={7},
  year={2010}
}

@article{barton2010b,
  title={A new model for extinction and recolonization in two dimensions: quantifying phylogeography},
  author={Barton, Nicholas H and Kelleher, Jerome and Etheridge, Alison M},
  journal={Evolution},
  volume={64},
  number={9},
  pages={2701--2715},
  year={2010},
  publisher={Wiley Online Library}
}
@article{veber2012,
author = {V{\'e}ber, A and Wakolbinger, A},
title = {The spatial {L}ambda-{F}leming-{V}iot process: an event-based construction and a lookdown representation},
year = {2014},
journal = {Annales de l'Institut Henri Poincar\'e},
pages={in press}
}

@article{tilman2011,
  title={Diversification, biotic interchange, and the universal trade-off hypothesis},
  author={D. Tilman},
  journal={The American Naturalist},
  volume={178},
  number={3},
  pages={355--371},
  year={2011},
  publisher={JSTOR}
}


@article{gernhard08,
  title={The conditioned reconstructed process},
  author={Gernhard, Tanja},
  journal={Journal of Theoretical Biology},
  volume={253},
  number={4},
  pages={769--778},
  year={2008},
  publisher={Elsevier}
}
@article{ayres12,
  title={BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics},
  author={Ayres, Daniel L and Darling, Aaron and Zwickl, Derrick J and Beerli, Peter and Holder, Mark T and Lewis, Paul O and Huelsenbeck, John P and Ronquist, Fredrik and Swofford, David L and Cummings, Michael P and others},
  journal={Systematic Biology},
  volume={61},
  number={1},
  pages={170--173},
  year={2012},
  publisher={Oxford University Press}
}

@article{ho11,
  title={Time-dependent rates of molecular evolution},
  author={Ho, Simon YW and Lanfear, Robert and Bromham, Lindell and Phillips, Matthew J and Soubrier, Julien and Rodrigo, Allen G and Cooper, Alan},
  journal={Molecular Ecology},
  volume={20},
  number={15},
  pages={3087--3101},
  year={2011},
  publisher={Wiley Online Library}
}


@article{fletcher10,
  title={The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection},
  author={Fletcher, William and Yang, Ziheng},
  journal={Molecular Biology and Evolution},
  volume={27},
  number={10},
  pages={2257--2267},
  year={2010},
  publisher={SMBE}
}


@article{degnan09,
  title={Gene tree discordance, phylogenetic inference and the multispecies coalescent},
  author={Degnan, J.H. and Rosenberg, N.A.},
  journal={Trends in Ecology \& Evolution},
  volume={24},
  number={6},
  pages={332--340},
  year={2009},
  publisher={Elsevier}
}
@article{best,
  title={{BEST}: Bayesian estimation of species trees under the coalescent model},
  author={Liu, L.},
  journal={Bioinformatics},
  volume={24},
  number={21},
  pages={2542--2543},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{lg4x,
  title={Modeling protein evolution with several amino acid replacement matrices depending on site rates},
  author={Le, Si Quang and Dang, Cuong Cao and Gascuel, Olivier},
  journal={Molecular Biology and Evolution},
  volume={29},
  number={10},
  pages={2921--2936},
  year={2012},
  publisher={SMBE}
}
@article{stem,
  title={{STEM}: species tree estimation using maximum likelihood for gene trees under coalescence},
  author={Kubatko, L.S. and Carstens, B.C. and Knowles, L.L.},
  journal={Bioinformatics},
  volume={25},
  number={7},
  pages={971--973},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{startbeast,
  title={Bayesian inference of species trees from multilocus data},
  author={Heled, J. and Drummond, A.J.},
  journal={Molecular Biology and Evolution},
  volume={27},
  number={3},
  pages={570--580},
  year={2010},
  publisher={SMBE}
}

@article{guindon10,
  title={Bayesian estimation of divergence times from large sequence alignments},
  author={Guindon, St{\'e}phane},
  journal={Molecular Biology and Evolution},
  volume={27},
  number={8},
  pages={1768--1781},
  year={2010},
  publisher={SMBE}
}

@article{guindon18,
  title={Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a ``Doubly Intractable'' Problem},
  author={Guindon, St{\'e}phane},
  journal={Systematic Biology},
  volume={67},
  number={},
  pages={651-661},
  year={2018},
}


%% Created for guindon at 2009-04-21 13:11:50 +1200 

@article{soubrier12,
  title={The influence of rate heterogeneity among sites on the time dependence of molecular rates},
  author={Soubrier, J. and Steel, M. and Lee, M.S.Y. and Sarkissian, C.D. and Guindon, S. and Ho, S.Y.W. and Cooper, A.},
  journal={Molecular Biology and Evolution},
  year={2012},
  publisher={SMBE}
}

%% Saved with string encoding Unicode (UTF-8) 
@article{matsen07,
  title={Phylogenetic mixtures on a single tree can mimic a tree of another topology},
  author={Matsen, F.A. and Steel, M.},
  journal={Systematic Biology},
  volume={56},
  number={5},
  pages={767--775},
  year={2007},
  publisher={Oxford University Press}
}
@book{bailey64,
  title={The elements of stochastic processes with applications to the natural sciences},
  author={Bailey, Norman TJ},
publisher={Wiley},
  year={1964}
}

@article{lemey2009,
  title={Bayesian phylogeography finds its roots},
  author={Lemey, Philippe and Rambaut, Andrew and Drummond, Alexei J and Suchard, Marc A},
  journal={PLoS Comput Biol},
  volume={5},
  number={9},
  pages={e1000520},
  year={2009},
  publisher={Public Library of Science}
}

@article{gillespie2011,
  title={Long-distance dispersal: a framework for hypothesis testing},
  author={Gillespie, R.G. and Baldwin, B.G. and Waters, J.M. and Fraser, C.I. and Nikula, R. and Roderick, G.K.},
  journal={Trends in Ecology \& Evolution},
  year={2011},
  vol=27,
  pages={47,56}
}

@article{guindon13,
  title={From trajectories to averages: an improved description of the heterogeneity of substitution rates along lineages.},
  author={Guindon, S.},
  journal={Systematic Biology},
  year={2013},
volume={62},
pages={22-34},
  publisher={Oxford University Press}
}

@article{arnold01,
Author = {Barry C. Arnold and Enrique Castillo and Jose Maria Sarabia},
Title = {Conditionally Specified Distributions: An Introduction},
Journal = {Statistical Science},
Year = 2001,
Volume = 16,
Pages = {249,265}
}

@article{arnold07,
	Author = {Barry C. Arnold and Enrique Castillo and Jose Maria Sarabia},
	Date-Added = {2009-04-21 13:08:07 +1200},
	Date-Modified = {2009-04-21 13:11:32 +1200},
	Journal = {Journal of Statistical Planning and Inference},
	Pages = {3249-3260},
	Read = {Yes},
	Title = {Variations on the classical multivariate normal theme},
	Volume = {137},
	Year = {2007},
	Bdsk-File-1 = {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}}


@article{boussau06,
  title={Efficient likelihood computations with nonreversible models of evolution},
  author={Boussau, Bastien and Gouy, Manolo},
  journal={Systematic biology},
  volume={55},
  number={5},
  pages={756--768},
  year={2006},
  publisher={Oxford University Press}
}

@article{boussau08,
	Abstract = {Fossils of organisms dating from the origin and diversification of cellular life are scant and difficult to interpret, for this reason alternative means to investigate the ecology of the last universal common ancestor (LUCA) and of the ancestors of the three domains of life are of great scientific value. It was recently recognized that the effects of temperature on ancestral organisms left 'genetic footprints' that could be uncovered in extant genomes. Accordingly, analyses of resurrected proteins predicted that the bacterial ancestor was thermophilic and that Bacteria subsequently adapted to lower temperatures. As the archaeal ancestor is also thought to have been thermophilic, the LUCA was parsimoniously inferred as thermophilic too. However, an analysis of ribosomal RNAs supported the hypothesis of a non-hyperthermophilic LUCA. Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two environmental-temperature-related phases during the evolutionary history of the tree of life. In the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea-Eukaryota; in the second period, it decreased. Therefore, the two lineages descending from the LUCA and leading to the ancestors of Bacteria and Archaea-Eukaryota convergently adapted to high temperatures, possibly in response to a climate change of the early Earth, and/or aided by the transition from an RNA genome in the LUCA to organisms with more thermostable DNA genomes. This analysis unifies apparently contradictory results into a coherent depiction of the evolution of an ecological trait over the entire tree of life.},
	Address = {Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite de Lyon, Universite Lyon I, 43 Boulevard du 11 Novembre, 69622 Villeurbanne, France.},
	Au = {Boussau, B and Blanquart, S and Necsulea, A and Lartillot, N and Gouy, M},
	Author = {Boussau, Bastien and Blanquart, Samuel and Necsulea, Anamaria and Lartillot, Nicolas and Gouy, Manolo},
	Crdt = {2008/11/28 09:00},
	Da = {20081218},
	Date-Added = {2009-01-30 16:18:39 +1300},
	Date-Modified = {2009-01-30 16:18:57 +1300},
	Dcom = {20090113},
	Dep = {20081126},
	Doi = {10.1038/nature07393},
	Edat = {2008/11/28 09:00},
	Issn = {1476-4687 (Electronic)},
	Jid = {0410462},
	Journal = {Nature},
	Jt = {Nature},
	Language = {eng},
	Mh = {Adaptation, Physiological/genetics/*physiology; Archaea/genetics/*physiology; Evolution, Molecular; Genes, rRNA/genetics; *Hot Temperature; Phylogeny},
	Mhda = {2009/01/14 09:00},
	Number = {7224},
	Own = {NLM},
	Pages = {942--945},
	Phst = {2008/03/05 {$[$}received{$]$}; 2008/09/01 {$[$}accepted{$]$}; 2008/11/26 {$[$}aheadofprint{$]$}},
	Pii = {nature07393},
	Pl = {England},
	Pmid = {19037246},
	Pst = {ppublish},
	Pt = {Journal Article; Research Support, Non-U.S. Gov't},
	Sb = {IM},
	So = {Nature. 2008 Dec 18;456(7224):942-5. Epub 2008 Nov 26. },
	Stat = {MEDLINE},
	Title = {Parallel adaptations to high temperatures in the Archaean eon.},
	Volume = {456},
	Year = {2008 Dec 18},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature07393}}

@article{dereeper08,
	Abstract = {Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The 'One Click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The 'Advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. The 'A la Carte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/},
	Author = {Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O.},
	Date-Added = {2009-01-19 17:02:10 +1300},
	Date-Modified = {2009-01-19 17:03:31 +1300},
	Journal = { Nucleic Acids Res.},
	Title = {Phylogeny.fr: robust phylogenetic analysis for the non-specialist.},
	Volume = {36},
	Year = {2008}}

@article{lartillot06,
	Author = {Nicolas Lartillot},
	Date-Added = {2008-12-18 09:36:03 +1300},
	Date-Modified = {2008-12-18 09:39:29 +1300},
	Journal = {Journal of Computational Biology},
	Pages = {1701-1722},
	Rating = {5},
	Title = {Conjugate Gibbs Sampling for Bayesian Phylogenetic Models },
	Volume = {13},
	Year = {2006},
	Bdsk-File-1 = {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}}

@book{aarts97,
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	Author = {E. Aarts and J. K. Lenstra},
	Publisher = {Wiley},
	Title = {Local search in combinatorial optimization},
	Year = 1997}

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	Author = {F. Abascal and R. Zardoya and D. Posada},
	Journal = {Bioinformatics},
	Pages = {2104-2105},
	Title = {ProtTest: selection of best-fit models of protein evolution},
	Volume = 21,
	Year = {2005}}

@phdthesis{adachi95,
	Author = {J. Adachi},
	School = {The Graduate University for Advanced Studies},
	Title = {Modeling of Molecular Evolution and Maximum Likelihood Inference of Molecular Phylogeny},
	Year = 1995}

@article{akaike74,
	Author = {H. Akaike},
	Journal = {IEEE Transactions on Automatic Control},
	Pages = {716-723},
	Title = {A new look at the statistical model identification},
	Volume = 19,
	Year = {1974}}

@article{amrine03,
	Author = {H. Amrine-Madsen and K Koepfli and R. Wayne and M. Springer},
	Journal = {Molecular Phylogenetics and Evolution},
	Pages = {225-240},
	Title = {A new phylogenetic marker, apolipoprotein {B}, provides compelling evidence for eutherian relationships},
	Volume = 28,
	Year = {2003}}

@article{ane05,
	Author = {C. An\'e and J. Burleigh and M. McMahon and M. Sanderson},
	Journal = {Molecular Biology and Evolution},
	Pages = {914-924},
	Title = {Covarion structure in plastid genome evolution: a new statistical test},
	Volume = 22,
	Year = {2005}}

@article{anisimova01,
	Author = {M. Anisimova and J. Bielawski and Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {1585-1592},
	Title = {The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites},
	Volume = 18,
	Year = {2001}}

@article{anisimova02,
	Author = {M. Anisimova and J. Bielawski and Z. Yang},
	Journal = {Molecular Biology and Evolution},
	Pages = {950-958},
	Title = {Accuracy and power of Bayes prediction of amino acid under positive selection},
	Volume = 19,
	Year = {2002}}

@article{anisimova03,
	Author = {M. Anisimova and R. Nielsen and Z. Yang},
	Journal = {Genetics},
	Pages = {1229-1236},
	Title = {Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.},
	Volume = 164,
	Year = {2003}}

@article{anisimova06,
	Author = {M. Anisimova and O. Gascuel},
	Journal = {Systematic Biology},
	Pages = {539-552},
	Title = {Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative},
	Volume = 55,
	Year = {2006}}

@article{anisimova07,
  title={Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites},
  author={Anisimova, Maria and Yang, Ziheng},
  journal={Molecular Biology and Evolution},
  volume={24},
  number={5},
  pages={1219--1228},
  year={2007},
  publisher={SMBE}
}

@article{anisimova11,
  title={Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes},
  author={Anisimova, M. and Gil, M. and Dufayard, J.F. and Dessimoz, C. and Gascuel, O.},
  journal={Systematic Biology},
  volume={60},
  number={5},
  pages={685--699},
  year={2011},
  publisher={Oxford University Press}
}



@article{atv,
	Author = {C. Zmasek and S. Eddy},
	Journal = {Bioinformatics},
	Pages = {383-384},
	Title = {{ATV}: display and manipulation of annotated phylogenetic trees},
	Volume = 17,
	Year = 2001}



@book{intro-algo,
	Author = {T. H. Cormen and C. E. Leiserson and R. L. Rivest},
	Chapter = { 17 greedy algorithms},
	Pages = {329-356},
	Publisher = {The Massachuset Institute of Technology Press},
	Title = {Introduction to algorithms},
	Year = 1992}

@article{seqgen,
	Author = {A. Rambaut and N.C. Grassly},
	Journal = {Computer Applications in the Biosciences (CABIOS)},
	Pages = {235-238},
	Title = {{S}eq-{G}en: an application for the {M}onte {C}arlo simulation of {DNA} sequence evolution along phylogenetic trees.},
	Volume = 13,
	Year = 1997}

@article{bailey02,
	Author = {J. Bailey and Z. Gu and R. Clark and K. Reinert and R. Samonte and S. Schwartz and M. Adams and E. Myers and P. Li and E. Eicher},
	Journal = {Science},
	Pages = {1003-1007},
	Title = {Recent segmental duplications in the human genome},
	Volume = 297,
	Year = 2002}

@article{baele06,
	Author = {G. Baele and J. Raes and Y. Van de Peer and S. Vansteelandt},
	Journal = {Molecular Biology and Evolution},
	Pages = {1397-1405},
	Title = {An improved statistical method for detecting heterotachy in nucleotide sequences},
	Volume = 23,
	Year = 2006}

@article{berry,
	Author = {V. Berry and O. Gascuel},
	Journal = {Theoretical Computer Science ({\`a} paraitre)},
	Title = {Inferring evolutionary trees with strong combinatorial confidence.},
	Year = 2000}

@article{kumar02,
	Author = {S. Kumar and S. Subramanian},
	Journal = {PNAS},
	Pages = {803-808},
	Title = {Mutation rates in mammalian genomes},
	Volume = {99},
	Year = {2002}}

@article{kumar96,
	Author = {Sudhir Kumar},
	Journal = {Molecular Biology and Evolution},
	Title = {A Stepwise Algorithm for Finding Minimum Evolution Trees},
	Year = 1996}

@article{nei97,
	Author = {Masatoshi Nei, Sudhir Kumar, and Kei Takahashi},
	Journal = {Special series of inaugural articles by members of the national academy of science},
	Pages = {584-593},
	Title = {The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids is small},
	Volume = 13,
	Year = 1997}

@article{nei98,
	Author = {M. Nei and S. Kumar and K. Takahashi},
	Journal = {PNAS},
	Pages = {12390-12397},
	Title = {The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small},
	Volume = 95,
	Year = 1998}

@inproceedings{abf96,
	Author = {R. Agarwala and V. Bafna and M. Farach and B. Narayanan                   and M. Paterson and M. Thorup},
	Booktitle = {Proceedings of the 7th Annual ACM-SIAM                    Symposium on Discrete Algorithms},
	Title = {On the approximability of numerical taxonomy:                   Fitting distances by tree metrics},
	Year = 1996}

@article{adell94,
	Author = {J. Adell and J. Dopazo},
	Journal = {Journal of Molecular Evolution},
	Pages = {305-309},
	Title = {{M}onte {C}arlo Simulation in phylogenies : An     application to Test the Constancy of Evolutionary Rates},
	Volume = 38,
	Year = 1994}

@incollection{adachi96,
	Address = {Tokyo},
	Author = {J. Adachi and M. Hasegawa},
	Booktitle = {Computer Science Monographs},
	Editor = {M. Ishiguro and G. Kitagawa and Y. Ogata and H. Takagi and Y. Tamura and T. Tsuchiya},
	Number = {28},
	Publisher = {The Institute of Statistical Mathematics},
	Title = {{MOLPHY} Version 2.3. Programs for molecular phylogenetics based on maximum likelihood},
	Year = 1996}

@article{adachi00,
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